From 2719f73b6813d11d13a9650cdd2ab8ec6e69385d Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 9 Jul 2022 15:43:36 +0100 Subject: gentoo resync : 09.07.2022 --- sci-biology/hmmer/Manifest | 6 +- .../hmmer-3.1_beta2-fix-header-install-path.patch | 89 ----------------- .../hmmer/files/hmmer-3.1_beta2-makefile.patch | 110 +++++++++++++++++++++ sci-biology/hmmer/hmmer-2.3.2-r4.ebuild | 75 -------------- sci-biology/hmmer/hmmer-2.3.2-r5.ebuild | 80 +++++++++++++++ sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild | 55 +++++++++++ sci-biology/hmmer/hmmer-3.1_beta2.ebuild | 49 --------- 7 files changed, 248 insertions(+), 216 deletions(-) delete mode 100644 sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch create mode 100644 sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch delete mode 100644 sci-biology/hmmer/hmmer-2.3.2-r4.ebuild create mode 100644 sci-biology/hmmer/hmmer-2.3.2-r5.ebuild create mode 100644 sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild delete mode 100644 sci-biology/hmmer/hmmer-3.1_beta2.ebuild (limited to 'sci-biology/hmmer') diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest index e041a677a3af..3e02058f5767 100644 --- a/sci-biology/hmmer/Manifest +++ b/sci-biology/hmmer/Manifest @@ -1,9 +1,9 @@ AUX hmmer-2.3.2-fix-build-system-destdir.patch 825 BLAKE2B 46264f43ed43a567c1f650710e1485942eb48a0b7ed3860424f00ca06cf04f9e923318c5df3d56eb312ed773bf2d42e22880b4ac6c2f81ac6c65bf2cebf44008 SHA512 f7eb3de5cbb1bf58b4ae4514e020ea059ad6a267e6f425494d8b444ac1bab056bc4709fed7f2793e68720b057ca1ac8c6dbca907125712d18dc05b77e37b1c3f AUX hmmer-2.3.2-fix-perl-shebangs.patch 2457 BLAKE2B 1afca014901d79416dac2c1d41e20371ef970aa3691a6b414e9a96adf8331c619753df7a42e1d9af63aab12a3fc8b8c7d2251129dd581bfb33a0d7c3e50970b2 SHA512 9597d77b3101c091bb1d005f36229cb6bedaf496a15da472495bb688fdb2750c94a38adc1236f3d90b0085caa78f61bddb350d51e0d3cc8dfa96edcdd5e2e5b9 -AUX hmmer-3.1_beta2-fix-header-install-path.patch 3202 BLAKE2B e6f8050c2edd11c890dc53bd6ba4cfaf6b537ab11ba45b88f497c0b62200029839df5f2adfa54612805ea87a5e252c9c198a52c1ba793a1c612ca99c3f8edb0b SHA512 ccaaff25a50a60526d0a16196b2b1d8cd57a7e9d016ce2b6b36ba1c0123966113b10965303dceb494810cd17a802514bba3a49d010ee6bbdc039715b84524d9a AUX hmmer-3.1_beta2-fix-perl-shebangs.patch 8605 BLAKE2B c0c78fed780b43df960dc24914e5dabe161243cec015deaf058d7eebf79c5e1633ded4f1305bb37b9766d74588009142fd58886e67810940e9601ef138647c21 SHA512 ce2c91c2d34d49dd5082a97ca0543bf3a176c792b4efd0cb37561114fc572b41d6cd546e16267283d33138ad54e2bb0c9c912c8fa1142e558a5452e9e72da2ff +AUX hmmer-3.1_beta2-makefile.patch 3679 BLAKE2B e258b23bda9d0515891f1d571b94f9ef48499f25ce6cb52c3d1bcd0a28bc527f335cb25ece944afb33e4824438315cc9986243fb13e07eb128d7859e0a77f4b1 SHA512 bebd36deee48d4a043a1d84233ccbc93de8e44b5f7f57bf24a551b53a6f3dbfb3166861555755744d0abb4fce871d7c19fa8887c08115b7d8f61ca5ad38c3cc6 DIST hmmer-2.3.2.tar.gz 1024933 BLAKE2B 34fdc7b24b28d653022c80a63b2fd8376c15c961e1550a04cb310943d165575a2721cc5e4cb516335f57414f8621b7e62c4e30ee1f107bb714e40c59ed37d418 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7 DIST hmmer-3.1b2.tar.gz 5965253 BLAKE2B 38d1d6fb43aa814c0e3ddc551469ebd6b967f181c45df3802598f31abef10998595218167555a8862c0d2caa9118d9a7f1c22b673b6d596665f797ba903093f5 SHA512 64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771 -EBUILD hmmer-2.3.2-r4.ebuild 1655 BLAKE2B ffc67289bc761e07d60df1d87e11abcc311b1fccc1652d542b71e0914660f3ed03e4a6e540d76d2c38e0d5cb43c606496da34fcac48bb84ee08c2a4822f0c562 SHA512 f07e067a72e388ebaff6c4712173bd6e68004a778c36823bcc685c7727a81ca77b448d046f2dec599b9c760b0c45fc379971beef227d2f6d43917a13e75b6abb -EBUILD hmmer-3.1_beta2.ebuild 1063 BLAKE2B a3469ebea515d16eb960fb5021ae7374b8736dbc0e0e933146f570478bf24cbfcee2eef59008126315669ab67cd70b569ddf401e07dd78b15a96e8d6b4329296 SHA512 fa75524ced910f633735ab72a1eb8d0ae0fd3ccc88dc12f98995b546fdd5084158509c8c99fe231450f5151dacc2b9477ee35090d9657401e47f8bd1dd0240b6 +EBUILD hmmer-2.3.2-r5.ebuild 1736 BLAKE2B 9ab5016f9a29c9d2dc22ed0456a064f14ea91c22d7a226aeeec02ad2c6766effb4a9933487aed37b335a113ab012829eb8aa583770e2ff01e934347445060a90 SHA512 18eb7ecb918ce4786ee1556fc641d1ca89c9255aa6009ea8b5d524752bad5046eeb50de9b0d5637b4c59cec624879d0c0f07698f5fe370aed7a25610aa377cca +EBUILD hmmer-3.1_beta2-r1.ebuild 1140 BLAKE2B a5a0a26f2461edc08101505fa600383952501083111e828b4a0484a2c895acb63b3784247ea3a9b4fb10a13089a84f09f9721b4835cbb7b5479f0877e62c84aa SHA512 65889b5afe47d60abdd7ebb4d098510e8f25979e442df2a88d6327ab2fffc6d056fa6f96f32c0d37614473bc961c1e60fc3e194e535c5b6816b3c420816c5ea9 MISC metadata.xml 262 BLAKE2B adaacf2ac22ce09f8b1b68f538773c1e2101156181ff302eca2ce1280ee5d45db4eb302a8eee1bbead5e55942443dd16ef924cfbfdc95a1658dc6a9f460468a2 SHA512 ac924b6b530d96645f173d40f7a2bf0e3abbf49048ebf7fadcea3dd553cd25504f0e68a103395de1fb59a2e5e11497dcead601be01cc6f0295ccbc4155f67e3f diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch deleted file mode 100644 index b9ff5b92b8f9..000000000000 --- a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch +++ /dev/null @@ -1,89 +0,0 @@ -Install headers into 'hmmer3' subdir and not into global includedir. - ---- a/easel/Makefile.in -+++ b/easel/Makefile.in -@@ -465,11 +465,12 @@ - ${INSTALL} -d ${DESTDIR}${bindir} - ${INSTALL} -d ${DESTDIR}${libdir} - ${INSTALL} -d ${DESTDIR}${includedir} -+ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 - ${INSTALL} -m 0644 libeasel.a ${DESTDIR}${libdir}/ - for file in ${HDRS}; do\ -- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ -+ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ - done -- ${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/ -+ ${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/hmmer3/ - ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} install - - # "make uninstall" reverses the steps of "make install" ---- a/Makefile.in -+++ b/Makefile.in -@@ -143,6 +143,7 @@ - ${INSTALL} -d ${DESTDIR}${bindir} - ${INSTALL} -d ${DESTDIR}${libdir} - ${INSTALL} -d ${DESTDIR}${includedir} -+ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 - ${INSTALL} -d ${DESTDIR}${man1dir} - ${INSTALL} -d ${DESTDIR}${pdfdir} - ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} install ---- a/src/impl_dummy/Makefile.in -+++ b/src/impl_dummy/Makefile.in -@@ -152,8 +152,9 @@ - ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} - - install: -+ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 - for file in ${HDRS}; do \ -- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ -+ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ - done - - uninstall: ---- a/src/impl_sse/Makefile.in -+++ b/src/impl_sse/Makefile.in -@@ -155,8 +155,9 @@ - - - install: -+ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 - for file in ${HDRS}; do \ -- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ -+ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ - done - - uninstall: ---- a/src/impl_vmx/Makefile.in -+++ b/src/impl_vmx/Makefile.in -@@ -152,8 +152,9 @@ - ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} - - install: -+ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 - for file in ${HDRS}; do \ -- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ -+ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ - done - - uninstall: ---- a/src/Makefile.in -+++ b/src/Makefile.in -@@ -322,15 +322,16 @@ - ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} - - install: -+ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 - ${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} install - for file in ${PROGS}; do \ - ${INSTALL} -m 0755 $$file ${DESTDIR}${bindir}/ ;\ - done - ${INSTALL} -m 0755 libhmmer.a ${DESTDIR}${libdir}/ - for file in ${HDRS}; do \ -- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ -+ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ - done -- ${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/ ;\ -+ ${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/hmmer3/ ;\ - - uninstall: - ${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} uninstall diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch new file mode 100644 index 000000000000..1c08d67e7bdd --- /dev/null +++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch @@ -0,0 +1,110 @@ +* Install headers into 'hmmer3' subdir and not into global includedir +* Respect AR + +--- a/easel/Makefile.in ++++ b/easel/Makefile.in +@@ -465,11 +465,12 @@ + ${INSTALL} -d ${DESTDIR}${bindir} + ${INSTALL} -d ${DESTDIR}${libdir} + ${INSTALL} -d ${DESTDIR}${includedir} ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + ${INSTALL} -m 0644 libeasel.a ${DESTDIR}${libdir}/ + for file in ${HDRS}; do\ +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ + done +- ${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/ ++ ${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/hmmer3/ + ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} install + + # "make uninstall" reverses the steps of "make install" +--- a/libdivsufsort/Makefile.in ++++ b/libdivsufsort/Makefile.in +@@ -16,7 +16,7 @@ + CFLAGS = @CFLAGS@ @PTHREAD_CFLAGS@ @PIC_FLAGS@ + CPPFLAGS = @CPPFLAGS@ + MPILIBS = @MPILIBS@ +-AR = @AR@ rc ++AR = @AR@ + RANLIB = @RANLIB@ + INSTALL = @INSTALL@ + +@@ -43,7 +43,7 @@ + + + libdivsufsort.a: $(OBJS) +- ${QUIET_AR}${AR} libdivsufsort.a $(OBJS) ++ ${QUIET_AR}${AR} rc libdivsufsort.a $(OBJS) + @${RANLIB} libdivsufsort.a + @chmod 644 libdivsufsort.a + +--- a/Makefile.in ++++ b/Makefile.in +@@ -143,6 +143,7 @@ + ${INSTALL} -d ${DESTDIR}${bindir} + ${INSTALL} -d ${DESTDIR}${libdir} + ${INSTALL} -d ${DESTDIR}${includedir} ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + ${INSTALL} -d ${DESTDIR}${man1dir} + ${INSTALL} -d ${DESTDIR}${pdfdir} + ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} install +--- a/src/impl_dummy/Makefile.in ++++ b/src/impl_dummy/Makefile.in +@@ -152,8 +152,9 @@ + ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} + + install: ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + for file in ${HDRS}; do \ +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ + done + + uninstall: +--- a/src/impl_sse/Makefile.in ++++ b/src/impl_sse/Makefile.in +@@ -155,8 +155,9 @@ + + + install: ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + for file in ${HDRS}; do \ +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ + done + + uninstall: +--- a/src/impl_vmx/Makefile.in ++++ b/src/impl_vmx/Makefile.in +@@ -152,8 +152,9 @@ + ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} + + install: ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + for file in ${HDRS}; do \ +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ + done + + uninstall: +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -322,15 +322,16 @@ + ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} + + install: ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + ${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} install + for file in ${PROGS}; do \ + ${INSTALL} -m 0755 $$file ${DESTDIR}${bindir}/ ;\ + done + ${INSTALL} -m 0755 libhmmer.a ${DESTDIR}${libdir}/ + for file in ${HDRS}; do \ +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ + done +- ${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/hmmer3/ ;\ + + uninstall: + ${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} uninstall diff --git a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild deleted file mode 100644 index a58b60f93288..000000000000 --- a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -DESCRIPTION="Sequence analysis using profile hidden Markov models" -LICENSE="GPL-2" -HOMEPAGE="http://hmmer.org/" -SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz" - -SLOT="2" -IUSE="altivec test threads" -RESTRICT="!test? ( test )" -KEYWORDS="~amd64 ~x86" - -DEPEND="test? ( dev-lang/perl )" -RDEPEND="" - -PATCHES=( - "${FILESDIR}/${P}-fix-perl-shebangs.patch" - "${FILESDIR}/${P}-fix-build-system-destdir.patch" -) - -src_configure() { - # prevent stray environmental variable - # from causing issues in the test phase - unset TMPDIR - - econf \ - --enable-lfs \ - $(use_enable altivec) \ - $(use_enable threads) -} - -src_install() { - default - - newlib.a src/libhmmer.a libhmmer2.a - insinto /usr/include/hmmer2 - doins src/*.h - - dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate} - dolib.a squid/libsquid.a - insinto /usr/include/hmmer2 - doins squid/*.h - - dodoc NOTES Userguide.pdf - newdoc 00README README - - # rename files due to collisions with hmmer-3 - # in order to make SLOTing possible - local i - - # first rename man pages... - pushd "${ED%/}"/usr/share/man/man1/ >/dev/null || die - for i in hmm*.1; do - mv ${i%.1}{,2}.1 || die - done - popd >/dev/null || die - - # ... then rename binaries - pushd "${ED%/}"/usr/bin/ >/dev/null || die - for i in hmm*; do - mv ${i}{,2} || die - done - popd >/dev/null || die -} - -pkg_postinst() { - elog "All ${P} binaries have been renamed, in order" - elog "to avoid collisions with hmmer-3. For instance" - elog - elog " hmmalign -> hmmalign2" - elog -} diff --git a/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild new file mode 100644 index 000000000000..b9f77b9dfce8 --- /dev/null +++ b/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="Sequence analysis using profile hidden Markov models" +HOMEPAGE="http://hmmer.org/" +SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="2" +KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_ppc_altivec test" +RESTRICT="!test? ( test )" + +BDEPEND="test? ( dev-lang/perl )" + +PATCHES=( + "${FILESDIR}/${P}-fix-perl-shebangs.patch" + "${FILESDIR}/${P}-fix-build-system-destdir.patch" +) + +src_configure() { + # prevent stray environmental variable + # from causing issues in the test phase + unset TMPDIR + + econf \ + --enable-lfs \ + --enable-threads \ + $(use_enable cpu_flags_ppc_altivec altivec) +} + +src_compile() { + emake AR="$(tc-getAR) rcs" +} + +src_install() { + default + + newlib.a src/libhmmer.a libhmmer2.a + insinto /usr/include/hmmer2 + doins src/*.h + + dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate} + dolib.a squid/libsquid.a + insinto /usr/include/hmmer2 + doins squid/*.h + + dodoc NOTES Userguide.pdf + newdoc 00README README + + # rename files due to collisions with hmmer-3 + # in order to make SLOTing possible + local i + + # first rename man pages... + pushd "${ED}"/usr/share/man/man1/ >/dev/null || die + for i in hmm*.1; do + mv ${i%.1}{,2}.1 || die + done + popd >/dev/null || die + + # ... then rename binaries + pushd "${ED}"/usr/bin/ >/dev/null || die + for i in hmm*; do + mv ${i}{,2} || die + done + popd >/dev/null || die +} + +pkg_postinst() { + elog "All ${P} binaries have been renamed, in order" + elog "to avoid collisions with hmmer-3. For instance" + elog + elog " hmmalign -> hmmalign2" + elog +} diff --git a/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild new file mode 100644 index 000000000000..666d21cd5532 --- /dev/null +++ b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +MY_PV="${PV/_beta/b}" + +DESCRIPTION="Sequence analysis using profile hidden Markov models" +HOMEPAGE="http://hmmer.org/" +SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz" +S="${WORKDIR}/${PN}-${MY_PV}" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="cpu_flags_ppc_altivec cpu_flags_x86_sse gsl mpi test" +RESTRICT="!test? ( test )" + +RDEPEND=" + mpi? ( virtual/mpi ) + gsl? ( sci-libs/gsl:= )" +DEPEND="${RDEPEND}" +BDEPEND="test? ( dev-lang/perl )" + +PATCHES=( + "${FILESDIR}"/${PN}-3.1_beta2-fix-perl-shebangs.patch + "${FILESDIR}"/${PN}-3.1_beta2-makefile.patch +) + +src_configure() { + # make build verbose, bug #429308 + export V=1 + + econf \ + --disable-pic \ + --enable-threads \ + $(use_enable cpu_flags_ppc_altivec vmx) \ + $(use_enable cpu_flags_x86_sse sse) \ + $(use_enable mpi) \ + $(use_with gsl) +} + +src_compile() { + emake AR="$(tc-getAR)" +} + +src_install() { + default + dodoc Userguide.pdf + + insinto /usr/share/hmmer + doins -r tutorial +} diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild deleted file mode 100644 index b65fa0824f9b..000000000000 --- a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MY_PV="${PV/_beta/b}" - -DESCRIPTION="Sequence analysis using profile hidden Markov models" -HOMEPAGE="http://hmmer.org/" -SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads" -RESTRICT="!test? ( test )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" - -RDEPEND=" - mpi? ( virtual/mpi ) - gsl? ( sci-libs/gsl:= )" -DEPEND="${RDEPEND} - test? ( dev-lang/perl )" - -S="${WORKDIR}/${PN}-${MY_PV}" -PATCHES=( - "${FILESDIR}/${PN}-3.1_beta2-fix-perl-shebangs.patch" - "${FILESDIR}/${PN}-3.1_beta2-fix-header-install-path.patch" -) - -src_configure() { - # make build verbose, bug 429308 - export V=1 - - econf \ - --disable-pic \ - $(use_enable altivec vmx) \ - $(use_enable cpu_flags_x86_sse sse) \ - $(use_enable mpi) \ - $(use_enable threads) \ - $(use_with gsl) -} - -src_install() { - default - dodoc Userguide.pdf - - insinto /usr/share/${PN} - doins -r tutorial -} -- cgit v1.2.3